How to make all faces flip to the right/consistent direction?
TL;DR: Select all and press ShiftN to Recalculate Normals (CtrlN in 2.7x and earlier).

I think this is problem you are having: some of the normals are always facing the wrong direction.
If you have the whole mesh selected when you flip normals then you are just toggling between the backwards faces and the correct faces, what faces are backwards. You are flipping the whole mesh, the correct parts will become backwards.
Whilst in Edit Mode, with the whole mesh selected, Recalculate the normals. That should fix the problem.
If recalculating the normals does not fix it, then you will have to go through your mesh and select only the faces that are backwards then flip normals.
I think you want the inside of the scope to point towards the inside. That is a case where Recalculate will probably not work. If the inside cylinder is unconnected from the rest of the mesh, then just hover the mouse over the inner cilinder and press L.